I'm new to running SAIGE-gene and would like to add sequencing batch as a covariate. May I know if these batches could be coded as a categorical variable (either as "batch1" or numeric factors) or do they need to be in a form of a design matrix where each batch is separated into different columns coded with either 1 or 0 in the covariate file as in the example below?
Hi Dr. Zhou,
Thank you for developing SAIGE.
I'm new to running SAIGE-gene and would like to add sequencing batch as a covariate. May I know if these batches could be coded as a categorical variable (either as "batch1" or numeric factors) or do they need to be in a form of a design matrix where each batch is separated into different columns coded with either 1 or 0 in the covariate file as in the example below?
Cheers, Tze Yin